A Legacy in Progress
by Wings of a Wolf
Summary: For a month after the Battle of New York, Bruce Banner has been sequestered in Stark Tower's Research and Development. Somehow, he ends up staying far longer than that, longer than anyone could have expected. He and Tony end up building (with a little help from their friends and Fury) the greatest legacy of all: the Avengers Initiative, fully realized. Tony Stark/Bruce Banner.
1. The Invitation

**The Invitation**

It only took a couple days of knowing Tony for Bruce to realize that Tony was obsessed. Tony had programs running constantly, seeking out any and all involvement of Stark Industries weapons, anywhere in the world, used by anyone that he hadn't sanctioned. After getting even the slightest ping, he would go tearing off without any plan or forewarning. Sometimes the only notice Bruce or Pepper had was when Tony finally returned and was being patched up by Dummy with Jarvis making noises of disapproval in the background. Pepper tried her best to throw distractions in his way, and Bruce himself had been a distraction until Tony had gotten used to having a green monster cum gamma ray specialist around. Pepper could only do so much, and Bruce wasn't comfortable enough with his place at the Tower to start helping her out.

A month after the Battle of New York, it became imminently clear that Tony wasn't sleeping. He still had scrapes all over from the battle and a splint on one of his toes where it had broken in a landing. Three times, Bruce had gone upstairs to Research and Development in his own nightly travels- being on the run had made him something of a light sleeper, more of a catnapper, really- and Tony had been awake every time.

"Can't sleep?" he asked, hesitantly.

Tony's hands were wrapped around a white and black Stark Industries mug. He reached up only to manipulate a computer display idly, adjusting designs on what looked like one of the repulsors in the gloves.

"You're one to talk, Brucie Boy," Tony said, closing out of the display in what seemed like instinct more than conscious decision.

Bruce shrugged. There was a reason he tried not to question Tony too much on these things. He had his own secrets to hide. Sometimes, after all, Bruce still dreamed about swallowing a bullet. It wasn't like Fury's little mission changed anything- the world was the same as ever, business as usual, status quo still quo.

"I have trouble sleeping when I still half-expect the army to come bursting through the windows," he said dryly.

Tony twitched a finger at Dummy, who wheeled a pot of coffee over with more enthusiasm than care.

"As if anyone would dare crash my Tower. Well besides Agent-" Tony cut himself off, and what Bruce would almost call self-hatred, or perhaps as being slightly _too_ self-aware.

Bruce let it pass and took the coffee Dummy poured him. He stared down at it dubiously as the robot whirred and clicked at him. Tony made a tutting noise. "Don't think: drink."

"Your motto, sir," Jarvis interjected. Bruce stifled a laugh and took a sip of the coffee. He hated black coffee, and of course, Tony assumed that since he drank it black, everyone did. Regardless of whether he liked the coffee, caffeine in general was a bad idea for Bruce, as it elevated his heart rate and could easily cause an incident. He held the cup, but didn't take another sip.

"I was thinking that I should head out soon," Bruce said, tone quiet as he stared into the depths of his mug. "Maybe somewhere tropical this time, though an island might be a bad idea. Don't wanna trap the Other Guy up with other people that can't get away."

He could feel the weight of Tony's gaze on him, steady and thoughtful as he took the loudest possible sip of coffee. The noise drew Bruce's own eyes back up to meet his. "Or you could stay here," he suggested. "Might not have been in your long-term plans, 'cause you are obviously not used to thinking that far ahead, being on the run and all, but either Stark Industries or SHIELD would have plenty of work for you. Probably more than enough. I recommend signing on as a consultant. That way you wouldn't be tied to SHIELD if you need to leave again before we can get it sorted out. I don't trust SHIELD as far as I can throw 'em."

"I don't think any of us trust SHIELD as far as we can throw them." Fury had earned some of their grudging respect, for not rounding them all up and putting them under lock and key after the Battle. Only _some_ respect; the man would do whatever he believed was right, even if anyone else, including the people who were supposed to oversee him, thought it was wrong.

Bruce thought about it, imagined stepping back into a semi-normal life. A life with labs and research and probably working on the Super Soldier Serum again. A life with ID cards, limited access, and people using his research for God knew what. He didn't want to work for SHIELD, really. He didn't want to step back into that.

"What would _you_ want me to research?" Bruce asked.

Tony blinked at him, like he hadn't ever thought of that before. "I dunno. Whatever you want, really. I trust you."

Bruce paused. "All right."

* * *

Footnote- Being a radical and a renegade, I decided to stick my notes at the end of this chapter rather than at the the beginning. This is going to be a Verse. Capital V. That means that it will meander a bit, encompass many things, and overall fulfill all of my nasty Avengers-writing desires. I am hoping to do short updates often, but make no promises regarding the words "short" or "often." I've listed the main pairing as Tony Stark/Bruce Banner, but for the total list, I am including Phil Coulson/Clint Barton, Steve Rogers/Natasha Romanoff, and Happy Hogan/Pepper Potts. I am still pondering Thor, since I despise Jane, and if you take movie-verse alone, the relationship isn't exactly healthy. So, I will get back to you later, but I am considering Thor/Darcy Lewis. I am using the movie-verse as a frame and will fill in that frame with the comics as I see fit. I will be taking liberties. I do not apologize. I also can't promise I won't throw Loki in somewhere. There may even be an orgy. (There probably won't be an orgy.)


	2. Pet Projects

**Pet Projects**

When given an option, Bruce's first instinct at what to research for Tony was to attempt to cure himself. That was personal rather than professional, though, and Bruce didn't want anyone getting hold of the research that looking for a cure would entail, since it would all play nicely into the Super Soldier project. And besides, as long as he kept control, the Other Guy would, apparently, be glad to fight in the direction Bruce pointed rather than fight everyone in general. Bruce just had to keep control. Bruce liked control. Sometimes he wondered if that was the reason the Other Guy existed in the first place; maybe Bruce had liked control too much.

The question of how to help Tony's company kept Bruce up in his favorite R&D lab for hours, frowning at the information that gave him a hint at all of the pies Tony had stuck his fingers into. Weapons, of course, and energy, but also medicine, astrophysics, and genetic engineering. What had gotten Bruce in on the Super Soldier project (not that he'd known what it was) wasn't just his degree in physics, but the fact that he also had a degree in genetics. Combining the two enabled him to see the ways that gamma radiation might be applied to cellular regeneration and radiation resistance.

This got him thinking about Stark IntelliCrops. The crops were a very good step in the right direction. They had been invented as a fluff piece, essentially, to make the public focus on feeding the world's poor rather than on the shiny guns, but there was some decent underlying research there, for all that it had been mostly abandoned. IntelliCrops would grow anywhere and produced viable food, e.g. IntelliWheat, IntelliRice, etc, anywhere they were grown. But that was only if they managed to live out a full growth cycle. The crops would die sometimes overnight. There was a photograph of gigantic fields of dead stalks, a family of farmers looking bleak and hopeless in the background. In agricultural facilities with thousands of workers, they flourished, but on the small farms, where it really counted, they failed.

It was obvious Tony had no idea why. Tony's specialty was engineering, though he knew physics better than most trained physicists- and since Bruce knew the best physicists in the world, he could back up his claim that Tony was more intelligent than most of them on every level. But Tony wasn't a geneticist, and couldn't even begin to grasp why crops that could theoretically grow everywhere couldn't grow anywhere that wasn't a lab. Thus why the project had been abandoned.

Bruce leaned back in his chair, mind racing. He had seen so many starving people in his travels. The world was full of more hungry people than it knew what to do with. He could help. He knew he could.

"Jarvis, could you bring up all of the research on the IntelliCrops?"

"As you wish." Even as the AI spoke, images flooded the screen: detailed reports by heartbroken scientists that were carefully trying to hide that they were heartbroken, that years of research had come to nothing; photographs of cells dated from the project's beginning to its end; a map of what looked like the ideal cell; and pictures of the dead fields.

"Where is the research facility where this is housed, Jarvis?"

"In New Mexico, sir."

"Fun coincidence. Is the lab still up and running?"

"No, sir. The lab, known as the Stark Agricultural Research Facility, designation NGCH-4, was defunct as of 2009. Stark Industries has labeled the venture a total loss, and no one has entered the facility in three years."

"Could you get the samples associated with the reports transferred here?"

"Certainly, sir. They should arrive in approximately three days. Would you like me to inform Mr. Stark that you have chosen a project to work on?"

Bruce hesitated before saying, "No. Not yet. I don't even know if I can do anything yet."

"Very well, sir, though of course I won't be able to hide it from him if he asks."

"That's fine. Just… not yet, as long as he doesn't ask."

Three days later, a gigantic pile of boxes arrived for Bruce. Whoever Jarvis had pack them knew what they were doing, and everything was neatly labeled and carefully packaged.

Bruce appropriated his favorite lab and set to work.

"You took the consulting position at SHIELD after swearing up and down to me that you were better, that you no longer thought only of the next mission, that you were in a stable relationship now and _of course_ you wouldn't take unnecessary risks anymore. Do you remember that, Stark? Because I sure as hell do."

Tony linked his hands behind his head, pushing his chair back until he balanced it on two legs. "Somehow, every time I meet with you, I feel like I'm being interrogated. Why is that, Fury? No love for geniuses who moonlight as superheroes?"

"Stark…."

Tony waved off the growl like it was nothing. "I mean, I was exaggerating on the stable relationship thing, since Pepper hadn't even officially been with me on a date at that point, and she's moved on to greener pastures now, anyway. And I _am_ better. I'm always better; I'm the best, really-"

"Stark, you've been taking does weapons depots in your spare time, unsanctioned, wearing the suit that almost makes it seem like you _are_ sanctioned. I don't have time to deal with renegade Avengers who cause international SNAFUs and sulk like children when they're called to task."

Snorting, Tony said, "Please, Fury, let's be real here. I supported your Avengers Initiative when there was an Initiative to support, because it's really cool, and Dad liked him some superheroes, and I might owe him something 'cause he kind of, you know, saved my life with his entirely new awesome element, but your so-called 'Avengers' are completely scattered now, doing the 'lone gunman fight' thing, and one fight together under pressure does not a team make. And I get it. World Security Council is too scared to have us all in one city, because we're just that awesome, but don't talk like we're a team when there's no team."

Fury's eyes gleamed, like he had just tricked Tony into something, and he smiled the cold smile that always freaked Tony out hardcore.

"Well, unfortunately, my hands are tied, Mr. Stark. There can't _officially_ be an Avengers team. That would be too scary, after all." He stood. "No more weapons depots, Stark."

He left, and so did Tony. Tony's phone buzzed as he was leaving the building. Fury had sent him the most recent contact details for every one of the Avengers, including, to Tony's amusement, Bruce. "One down, five to go," Fury texted.

It was only when Tony did a mental count and got very, very confused that he realized Fury had included contact information for Agent Coulson.

* * *

Footnote- If I was going to be really proper, I would reformat and attach this to last chapter, but screw it. This is what happens when you serialize. Please review if you like it. Bonus points if anyone figures out what NGCH stands for. Review even if you don't like it, but I'll, uh, probably ignore you, since this is just for funsies anyway. ;P


	3. When Secrets Have Secrets

**When Secrets Have Secrets**

Bruce was asleep in one of the labs when Tony got back from SHIELD. It was around one in the afternoon and Bruce was slumped over a desk, surrounded by holograms of the IntelliCrops. Tony's tried not to smile. It seemed like Bruce had found his new obsession.

"How long has he been looking into the IntelliCrops, Jarvis?" Tony said, watching Bruce from the doorway.

"Approximately two weeks, sir. He has all of the research from NGCH-4, and has been attempting to discover the weak points in the cell structure. I believe he is only another week from creating the first test subject since the project was ended."

"Been a busy little bee, hasn't he?"

Tony approached Bruce, reaching out a hand. Bruce fell out of the chair.

He looked absolutely terrified, the heart monitor on his wrist beeping like mad and steadily climbing higher. Bruce looked at Tony, frowned, and didn't even bother to get up from the floor. He just closed his eyes. He took a breath, and his heart rate plummeted back from Hulk-territory to a more normal range.

"Handy trick," Tony commented.

Bruce opened his eyes, raising his brow in that "oh, so you're pretending you're smart now" way that he had. "What, the 'jumping out of my chair' or the control of my heart rate?"

"That was not a jump. That was a fall, mister. The heart rate. I never did figure out where you were hiding that huge bag of weed."

"If you haven't found it by now, and you still think I have it, aren't you worried about where I'm keeping it?" Bruce said dryly.

Tony smiled, delighted. He let the smile fade after a moment, trying not to think too hard about Bruce's fear- he really hadn't liked General Ross; General Ross was a big dick, or rather, a small dick, which was probably the problem in a Freudian kind of way- and said, "So Fury handed me these files, more or less told me to freelance the Avengers Initiative since his hands are tied by all that logistical government garbage, and told me where to find an alive!Coulson. Surprise?"

Bruce closed his eyes again. His heartbeat determinedly stayed the same.

"I assume there are details?"

"Well, yeah. Apparently, Coulson was dead for a while, but they injected him with one of the components of the Serum, and then he was in a coma for a while instead. He woke up a few days ago. This is from Fury's personal files; the official files don't even bother mentioning the Serum, since apparently the Serum is property of the Army and having any part of it connected with you means the government owns you."

Bruce's heart rate spiked. Tony kept half an eye on it, For Science. "I'm aware of that, thanks."

"Or at least thinks they own you. We're working on legislation and stuff, but it's a problem since everything is still really classified and all that jazz, but SHIELD and I are working on it." Tony clapped him on the shoulder, because he isn't even a little frightened of a big green man who saved him from crashing and burning and who talks science with him when he's not big and green.

Bruce looked achingly lost for a moment. "So, what does Fury want you to do?"

Tony decided not to answer directly. Bruce isn't a trophy or anything, but in some ways, Tony had been planning to collect all his favorite superheroes for a while now. "Jarvis, pull up the rebuild schematics. The Avengers suites."

A dazzling array of blueprints replaced the IntelliCrops. Bruce looked around, almost turning a full circle to see all of them. Each one is individually imprinted with the logos of all five Avengers- Steve, Thor, Bruce, Natasha, and Clint. Jeez, Coulson needed one now, didn't he? Tony didn't need a suite emblazoned with a logo. He had his name on the building, after all, and wasn't really one of the Avengers besides.

(Or was he? Fury had said "one down, five to go," not "two down, five to go," after all. But he had said Tony was a renegade Avenger. And did it matter what Fury thought if the Avengers Initiative no longer even belonged to SHIELD? Though, thinking that Fury didn't plan on keeping a hand in was naïve, which Tony was not.)

"What does this mean, Tony?" Bruce finally asked. His voice was soft, very soft, as he enlarged the blueprints for the suite Tony had planned for him. It had a private lab for Bruce's more sensitive experiments. There was a meditation room to the left of the living area, with a waterfall and bookshelves, because Bruce liked reading next to running water and books helped keep him calm anyway. The kitchenette had a sub-listing of all of Bruce's favorite foods that Jarvis should keep stocked. Tentative links had been added for furniture, including a ridiculously decadent bed and a small, 22" television for the living room, since Bruce didn't like the world to intrude too much in his private space.

"It means," Tony said, his tone equally soft, "that I want to know if I should contact Coulson or Rogers first, because we have no clue how to work together, and we have no guarantees that whoever survived in the gigantic army on the other side of that portal won't decide to take the long way to us. Gonna help me choose, Bruce?"

Bruce looked at him, then quirked a smile. "Of course I am. What would you do without me?"

Tony grinned, nodded. "Right. Science bros for life."

If Tony melts a little when Bruce smiles, that's just a private bro thing, _totally normal yo_, so there was no need to comment on it, really.

"Coulson," Bruce answered after a moment. "I didn't know him, but I got the distinct impression that he had been planning the Initiative for a while now, and he seemed like the kind of guy who would have plans about plans on how to make the Initiative actually functional. If we can get him to talk about it instead of keeping Fury' s secrets, it might work."

"Excellent. He's, uh, upstate, though."

Bruce didn't look as horrified at that as he expected. "Your point being?"

Tony shuddered. "There are cows up there."

"There are cows in India, too, Tony. Lots of cows. I don't think we need to be frightened of them."

"That's because you don't have Italian leather shoes," Tony pointed out. The simplest way to fix that would be not to wear the Italian leather shoes, but what is Tony, a heathen?

Bruce shakes his head. "When did you want to leave?"

"Tomorrow. I need to design the floor for Coulson if we're bringing him back with us, and I can't do _all_ of it on the way."

Bruce smiled a little at that, awkward and so charming that he probably vomited rainbows like a special, special unicorn. Tony decided it was time start work so that he didn't have to look at the rainbow-vomit that was Bruce anymore. "Jarvis, pull up the templates," Tony ordered. "Oh, Pepper is going to kill me if I don't get this building functional soon. Jarvis, make a note: no being killed should be on my agenda."

"That note has existed for quite a while, sir."

"Well, okay then. Where are the bots?"

"In your lab. You are in Dr. Banner's lab."

"Thanks for the heads-up, got it. Well, I guess I don't need them anyway. Coulson likes wine, right? We should get him a wine rack. Make a note, Jarvis. Or a wine cellar."

"A wine cellar would require him to travel over forty floors."

"Okay, nix the wine cellar."

Bruce shook his head and sneakily pulled up the IntelliCrops again.

"I see you doing that. You don't think I mind, do you? It's a good project, not that I can make any headway on it personally."

Startled, Bruce said, "I just didn't want to give you any false hopes, since I don't know if I can do anything yet either."

Tony shrugged. "Science is the business of hope, false or not. And hope isn't false unless you're lying about it. You just don't know yet- untested hypothesis, not the same thing, yada yada. Do you think Coulson would like to be close to or farther away from Barton and Natasha, given that he knows them better?"

Bruce stared at him for a moment (people always do that), then shakes his head ruefully. "You might leave him something to choose for himself, Tony."

"Okay, okay. Sure. So, no bright pink bathroom."

"I advise against it."

No one appreciated Tony's brilliance. Coulson would have looked _awesome_ in hot pink.

* * *

Footnote: I had this half-finished for quite a while, and then I started working on it again and tenses went all over the place. It was painful. I kept switching from past tense to present and it nearly drove me mad. I think I've been reading a lot in the present tense lately? And it kept getting longer, and I kept forgetting to actually use italics instead of manuscript format (underlining). I am not entire certain I caught all of the unintentional tense shifts. Ugh. I appreciate reviews, and warn everyone ahead of time that we're switching away from the science bros next chapter.


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